multiGSEA
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lianos
NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
I converted the GeneSetDb constructor to an S3 generic and exported it in 97e1b5c2bec010a04b321b706329e8f78176cace. The way it was done was the easiest to implement as it re-uses all the faux-s3...
The `eigenWeightedMean` is a pretty hand single-sample score, however its score can be driving by outliers with high expression. We can try calculating gene weights in the same way we...
The `recenter` parameter should enable the user to do: 1. "normal" row-wise mean-centering 2. provide a named vector of values to center each row 3. allow the user to specify...
Travis takes a super long time to build the environment to run the tests. Let's take inspiration from Dirk's patch to the tilledb-r [`.travis.yml` file](https://github.com/TileDB-Inc/TileDB-R/blob/master/.travis.yml) and configure it to use...
Looks like the Bioc folks will be going forward with this package-of-a-geneset container https://github.com/Kayla-Morrell/BiocSet Will see about moving GeneSetDb to that.
Currently we only support testing a specific contrast (either via a coefficient or a contrast vector), but we often do differential expression analysis where we want to test mean shifts...
A data.frame of features should be a fully featured input type for `x` in the `multiGSEA()` function. We should be able to use data.frame inputs to allow the user to...
The gs.order parameter looks to be broken, probably due to the powerful ComplexHeatmap refactoring that landed in Bioc3.9 (ComplexHeatmap v2)
Enable the user to define their own color palettes for the traces in iplot (density, in particular).
When genes are centered (with optional scaling), we lose a sense of what the abundance of the gene is. Think about adding an option to `mgheatmap` that adds a `rowAnnotation`...